Download DIsCOvERy sTuDIO® sCIENCE PORTFOlIO

DATASHEET
Discovery Studio®
Science Portfolio
From project conception, through to candidate selection, Discovery Studio® delivers a
comprehensive portfolio of validated scientific technologies. Built on a set of well-established
gold-standard applications backed by years of peer-reviewed publications (e.g., CHARMm, MODELER,
ZDock, Delphi, Catalyst, DMol3, TopKat, etc), in combination with novel leading-edge scientific tools,
Discovery Studio is ideally positioned to address today’s drug discovery challenges.
sCIENTIFIC SOFTWARE Portfolio
The Discovery Studio software portfolio is built on and powered by the enterprise-ready Pipeline Pilot
platform. This formidable architecture enables the scientist to effectively and efficiently conduct small and
macromolecule research within the following domains:
• Simulation: Perform calculations using Molecular Mechanics (MM), Molecular Dynamics (MD), Quantum
Mechanics (QM) and hybrid QM/MM
• Macromolecule Design and Analysis: Undertake sequence alignments and analysis, 3D structure prediction
(MODELER) and validation, structure ionization, predict protein-protein docking (ZDOCK), and even undertake
protein engineering and optimization of biophysical properties, including thermal stability and prediction of
protein aggregation.
• Small Molecule Design: Using a broad portfolio of scientific technologies, calculate ligand properties
and ligand efficiency, perform ligand profiling and filtering using well understood characteristics of drugs,
including permeability and undesirable feature metrics, and select optimal subsets using either molecular
diversity or cluster-based methods. In addition, it includes specialist tools for:
–– Pharmacophore Modeling: Specialist tools for small molecule screening and profiling. Includes tools
for both pharmacophore generation, validation and virtual screening, as well as ligand profiling.
–– Receptor-ligand Interactions: Undertake Structure-Based Design (SBD), including both fast and
physics-based ligand docking (also with flexible docking tools for both ligand and receptor side-chains),
combinatorial chemistry library design and optimization tools, fragment-based drug-design (FBDD) tools
and de novo ligand design.
• QSAR and ADMET: Create and validate statistical models against biologically important end-points.
Alternatively, make use of our pre-built validated models for a broad range of critical pharmacological endpoints, including: aqueous solubility, Blood-Brain Barrier penetration, intestinal absorption, Hepatotoxicity
and many more.
Delivered through a single, easy-to-use client interface, all of these scientific technologies can be
readily accessed in Discovery Studio® from both Windows and Linux environments.
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DATASHEET: Discovery Studio Science Portfolio
Simulation Products
Product
DS CHARMM
Description
Leverage this industry-standard program to study the energetics and flexibility of molecules - from small
ligands to multi-component physiological complexes, using the industry standard in force field technology,
CHARMM (Chemistry at HARvard Macromolecular Mechanics). DS CHARMm is regularly updated to include
the latest functionality developed by the CHARMM scientific community [e.g., Refs 1,2]. DS CHARMM
includes the following well-validated force fields (CHARMm, charmm27, charmm22, charmm19) and
solvation models such as Poisson-Boltzmann (PB), Generalized Born, Generalized Born with molecular
volume (GBMV) or simple switching (GBSW).
Examples of application of DS CHARMM include energy minimization and Molecular Dynamics simulations
of ligands and/or macromolecules, sampling of protein side-chain and loop flexibility, refinement and
calculation of protein-ligand interaction energies and even use in physics-based scoring of ligands in protein
active sites.
DS CHARMM is scalable for high throughput analysis of large numbers of ligands and can be accessed from
Discovery Studio, Pipeline Pilot and via command line for a greater degree of customization and flexibility.
CHARMM is maintained by the CHARMM Development Project, lead by Prof. Martin Karplus and his
lab at Harvard University. To learn more about CHARMM, please visit http://www.charmm.org/
DS CHARMM Lite
A customized version of CHARMm providing molecular minimization and energy calculation capabilities.
For example, with DS CHARMm Lite, perform in situ ligand minimization using the well-validated CHARMm
forcefields.
DS CHARMm is scalable for high throughput analysis of large numbers of ligands; all jobs can be run in
parallel and in background mode.
DS Analysis
Gain new insights into molecular processes by using DS Analysis to animate, graph, and tabulate results of
CHARMm molecular dynamics, small molecule docking, or protein modeling. Compute RMSD, hydrogen
bonds and contacts for thousands of docked ligand poses in a single job. Analyze and cluster MD trajectories
in an intuitive, easy-to-use manner. Calculate RMSD of residues/atoms during the course of a trajectory and
display the results in a dendrogram or heat map. Check the quality of the protein structure and analyze
regions with abnormalities using the ‘Protein Health’ toolpanel. Evaluate model quality based on the
MODELER DOPE (Discrete Optimized Protein Energy) energy function.
DS DMOL3MOLECULAR
DMol3 is a modeling program that uses density functional theory (DFT) to simulate chemical processes
and predict properties of materials both rapidly and accurately. DMol3 can predict processes in gas
phase, solution, and solid environments and is broadly applicable to research problems in chemistry,
pharmaceuticals, materials science, and chemical engineering, as well as solid state physics.
DS QUANTUMM
Increase accuracy of protein-ligand modeling during lead optimization by using accurate Quantum
Mechanics/Molecular Mechanics (QM/MM) methods that combine the Density-Functional Theory program
DS DMOL3 Molecular (QM) and CHARMm (MM). Perform single point energy calculations or geometry
optimization using a wide variety of exchange-correlation functionals and basis sets.
DS MMFF
Study the energetics and interaction between macromolecules and ligands with the industry-validated
forcefield MMFF94s that has been broadly parameterized for organic and bio-organic systems and for the
intermolecular interactions crucial to enzyme binding.
DS CFF
Optimize DNA, RNA, carbohydrates, lipids, proteins, peptides, and small-molecule models with high
confidence on accuracy of results. The forcefield parameters in CFF (Consistent Forcefield) were developed
by computing the properties of 1,768 different molecules spanning 19,432 molecular structures, resulting in
a robust and diverse collection of parameters applicable to most biomolecules and small molecules.
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DATASHEET: Discovery Studio Science Portfolio
Macromolecule-based Design and Analysis Products
Product
DS SEQUENCE
ANALYSIS
Description
With DS Sequence Analysis, use the popular BLAST and PSI-BLAST algorithms to identify homologs for
protein sequences by searching databases that are either installed locally or available via the internet at
NCBI. In addition, access tools for performing phylogenetic analysis and Evolutionary Trace analysis.
For Antibody Modeling, use pre-compiled CDR loop databases to automate the process of CDR
identification and annotation. A sequence alignment file of the best aligned hits enables automated loop
grafting of the CDR regions.
DS Biopolymer
Biopolymer delivers model building and electrostatics analysis tools for use with nucleic acids (DNA, RNA),
proteins and peptides. Calculate electrostatic potentials and solvation energies of both large and small
molecules using Poisson-Boltzmann electrostatics (DelPhi3,4). Calculate the protonation state of titratable
amino acids within the protein quickly and accurately, using the Generalized Born model for charge
estimation, and accurately predicts pK’s, pH titration curves, and overall energy of folding. In the area of X-ray
crystallography, build protein models (with X-BUILD technology) and fit ligands (with X-LIGAND technology)
into X-ray electron density maps.
DelPhi is developed and maintained by the lab of Prof. Barry Honig
at Columbia University. To learn more about DelPhi, please visit
http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:DelPhi
DS MODELER
Automatically and rapidly generate a refined homology model of a protein, given only the sequence
alignment to a known 3D protein structure, with the industry-standard MODELLER algorithm5, 6, 7, 8 for fast
homology modeling. With DS MODELER, you can build protein models and mutants with ligands bound,
perform loop modeling, perform structure-based alignments, create sequence profiles and perform remote
homology modeling searching. DS MODELER also features SALIGN, a method for improving the sequence
alignment in low homology cases that uses sequence profile information.
In the domain of antibody modeling, additional automation tools are included to facilitate both Full-length
(Immunoglobulin G templates for IgG1 and IgG2), and Framework-based model building.
MODELLER is maintained by the team of Prof. Andrej Sali at the University of California, San
Francisco (UCSF). To learn more about MODELLER, please visit http://salilab.org/modeller/
DS PROTEIN REFINE
Optimize a loop region of a protein structure using an in-house developed algorithm based on CHARMm.
Generate multiple energy optimized variants of the loop region and browse through loop structures
and chart results. In addition, optimize the side-chain of a protein structure using an in-house developed
algorithm based on a systematic searching method and CHARMm energy minimization. Both optimization
algorithms have no dependency on initial structure (ab initio approach).
DS PROTEIN HEALTH
Access the validity of a protein structure (or part of the structure) derived from modeling studies or
experimental data. Protein Health uses a method called Profiles-3D Verify to evaluate the protein structure
by comparing its structural environments with the preferred environments of amino acids. Misfolded
protein segments within a protein structure can be identified by this method, indicating where additional
consideration should be given to structural packing. In addition, check the quality of the protein structure
and analyze regions with abnormalities using the ‘Protein Health’ tool panel.
DS PROTEIN FAMILIES
Gain a better understanding of the mechanism of protein function at the molecular level by analyzing
the sequence conservation patterns within a family of protein sequences, as well as the position of those
conserved residues on the 3D structure. Includes tools to align a family of proteins based on sequence
or structure, perform phylogenetic analysis and Evolutionary Trace analysis using a hierarchical clustering
method and map information onto your 3D structure.
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DATASHEET: Discovery Studio Science Portfolio
Macromolecule-based Design and Analysis Products (continued)
Product
Description
DS PROTEIN DOCKING
Predict protein-protein structure interactions of novel targets rapidly and accurately with DS Protein
Docking. Perform rapid rigid body docking with the well-published ZDOCK algorithm9,10, which employs an
FFT-based method using a pair-wise shape complementarity function for identifying docked conformations
and scores hits based on atomic contact energies. Increase the accuracy of docked poses using the
ZRANK scoring function11. Use the RDOCK algorithm12 to refine ZDOCK hits based on a CHARMm energy
minimization and score poses by CHARMm energy and desolvation energy. Narrow the search and identify
poses of interest with advanced clustering methods.
ZDock, ZRank and RDock are developed and maintained by the lab of Dr. Zhiping
Weng at the University of Massachusetts Medical School. To learn more about
ZDock, ZRank and RDock, please visit http://zlab.umassmed.edu/
DS Protein
Aggregation
Identify the size and location of regions on antibodies prone to aggregation, and then predict mutations
leading to improved stability. Uses the spatial aggregation propensity algorithm13, 14 [WO 2009/155518 A1]15
Additionally, DS Protein Aggregation can be used to identify surface regions on proteins, likely to be involved
in protein-protein bindings events16.
The spatial aggregation propensity algorithm is maintained and developed by
the lab of Prof. Bernhardt Trout at the Massachusetts Institute of Technology. To
learn more about it, please visit http://web.mit.edu/troutgroup/
DS X-RAY
Contains interactive and semi-automated tools for the model building, analyis and refinement stage of
crystallographic (X-ray) structure determination. Capabilities include CNX protocols for structure refinement,
water picking, and structure validation. Includes CNX Standalone.
Small Molecule Pharmacophore Products
Product
Description
DS Catalyst Search
Use DS Catalyst Search to carry out rapid database searches with a pre-defined or customized
pharmacophore query. Includes the ability to handle a range of match constraints, including partial,
minimum number and required feature matches. Results can include. Additionally, can either search
compounds using a flexible match, or use multiple pre-computed rigid conformer samples.
DS Catalyst DB Build
Easily create a 3D compound database for querying pharmacophore models and identifying potential lead
compounds. With DS Catalyst Build, convert compounds into a 3D database that stores a diverse sampling of
all the energetically accessible conformations under physiological conditions for any given structure.
DS Catalyst
Conformation
Rapidly calculate conformational models for small molecules that provide diverse representations of
all the molecule’s energetically accessible conformations. Choose from among three conformation
generators (CAESAR, FAST, BEST) to select the algorithm that is best suited to each drug discovery project.
Within each algorithm, parameters can be customized to optimize the conformational sampling. From
these generated conformers, create pharmacophore hypotheses for querying compound libraries of both
rigid and flexible molecules.
DS Catalyst
Hypothesis
Automatically create qualitative or quantitative pharmacophore models that identify the essential chemical
and structural features required for target binding. Includes capabilities to automatically generate common
feature pharmacophore hypotheses from sets of known active ligands (HIPHOP) and also structure-activity
relationship-based models when activity data is provided (HypoGen). Model refinements can be delivered
with inclusion of exclusion volumes (HIPHOPREFINE and HypoGenRefine, respectively). A further feature
is that test sets containing examples of known active and inactive ligands can be used to validate the
predictive potential of each pharmacophore model.
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DATASHEET: Discovery Studio Science Portfolio
Small Molecule Pharmacophore Products (continued)
Product
Description
DS Catalyst SBP
DS Catalyst SBP provides tools for fast and easy creation of structure-based pharmacophore (SBP) models
from the putative binding site in a protein, either from receptor-ligand complex, or directly from a structure
if no bound ligand information is available. Notably, with DS Catalyst SBP, protein structure pharmacophore
features can be combined directly with ligand features to create a more complete model of the features
critical for binding.
DS Catalyst Score
Enables hit results from a pharmacophore screen to be evaluated and prioritized. DS Catalyst Score
calculates the predicted fit or activity value for each compound. Based on the size of your returned search hit
list, have the flexibility to broaden or narrow your search results by specifying the minimum and maximum
feature requirements of your pharmacophore model.
DS Catalyst Shape
Expand or refine a search query using a 3D shape representation from a molecule from a specified
conformation. Shape queries can be used to identify molecules that possess a similar shape with or without
considering specific chemical entities. Because overall shape is considered, the search hits can exhibit a far
greater topological diversity than standard 2D searches.
HYPODB
HypoDB is a database of high-quality pharmacophore models from Inte:Ligand containing 1846 individual
pharmacophore models from 187 targets. The database can be used to explore the selectivity and specificity
of candidate compounds across a wide variety of therapeutically relevant targets. This method of profiling
can also help identify potential mechanism of action, potential adverse targets or new targets for candidate
drug compounds.
Receptor-Ligand Interaction Products
Product
CDOCKER
(via DS CHARMM)
Description
Dock ligands using the validated CDOCKER algorithm, a grid-based molecular docking method17 that
employs CHARMm. With CDOCKER, initial ligand conformations are sampled via high temperature
molecular dynamics and are also allowed to flex during the refinement (via simulated annealing MD).
Crucially, CDOCKER also provides a physics-based scoring function, via the CHARMm energy of the docked
complex.
CDOCKER has been shown to give highly accurate docked poses18. DS CHARMM is scalable for high
throughput analysis of large numbers of ligands and can be accessed from Discovery Studio and Pipeline Pilot
DS FLEXIBLE DOCKING Perform rational flexible docking that combines the strength of CHARMm for accurate receptor sampling
with efficient, features-based docking.19 DS Flexible Docking is a realistic approach to flexible docking in
which the docking of small molecules is influenced by existing low-energy conformations of side chains in
the active site. DS Flexible Docking can be parallelized in multi-core machines or compute clusters for virtual
high-throughput screening.
DS LIBDOCK
Perform efficient docking by using polar and apolar features (hotspots) on the receptor binding site to guide
docking. Use the industry-standard Catalyst engine to generate small molecule conformations (DS Catalyst
Conformation, optional but strongly recommended) to increase accuracy of docking. DS LibDock can be
parallelized in multi-core machines or compute clusters for virtual high-throughput screening.
DS LIGANDFIT
Gain direct insight into the complementary features of ligands and their potential as lead candidates. DS
LigandFit lets you easily dock ligands into the binding site of receptors using shape-based searching and
Monte Carlo sampling of ligands. Parameters are customizable, and your settings can be saved and shared
with other users. DS LigandFit can be parallelized in multi-core machines or compute clusters for virtual
high-throughput screening.
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DATASHEET: Discovery Studio Science Portfolio
Receptor-Ligand Interaction Products (continued)
Product
Description
DS LIGANDSCORE
Evaluate ligand-protein interactions with well-validated and trained scoring functions and their individual
descriptors. Insight gained with DS LigandScore will help you identify potential problems in a binding mode
hypothesis, discriminate between correct and incorrect poses from docking, and prioritize posed ligands for
downstream efforts such as screening or synthesis. Parameters are customizable and your settings can be
saved and shared with other users. DS LigandScore can be parallelized in multi-core machines or compute
clusters for virtual high-throughput screening.
DS LIBRARY DESIGN
DS Library Design provides a full suite of similarity and diversity clustering methods specifically tailored for
chemical library design. Use Pareto Optimization methods to optimize multiple properties within a chemical
library design. All protocols within this package are designed to select the most effective chemical libraries,
and members within those libraries, for specific research projects.
DS MCSS
Multiple Copy Simultaneous Search (MCSS20,21,22) is a fragment docking methodology that can be used
to characterize and analyze binding sites. Multiple fragment copies are randomly distributed in a binding
site sphere and CHARMm minimizations are performed to find the most favorable fragment positions. The
placed fragments are sorted by the MCSS_Score.
MCSS was originally developed by Prof. Martin Karplus and his lab at Harvard University.
DS LUDI
Rapidly identify drug-like scaffolds with DS Ludi, a de novo drug discovery application that uses interaction
sites in the receptor binding pocket to search fragment libraries and identify and rank molecules.
DS Ludi’s robust set of design tools allows you to simulate screening before performing experimental assays,
to explore libraries of commercially-available ligand scaffolds, and to modify existing ligands by scoring
candidate derivatives in the receptor binding site. DS Ludi contains a library of drug-like fragments, but also
gives the ability to add custom fragments.
DS De Novo Evolution
Generate complete, drug-like molecules with DS De Novo Evolution by linking and growing fragments onto
a scaffold. Choose from three modes that are optimized for either speed or accuracy: In Quick mode, a single
best scoring inhibitor is suggested after each generation ranked by any one of the DS Ludi (pre-requisite)
or DS LigandScore (optional) scores. In Full Evolution mode, survivors are selected from generations of
inhibitors. In Combinatorial mode, all combinations of derivatives of the scaffold are enumerated.
DS De Novo
Ligand Builder
DS De Novo Ligand Builder is a unique fragment based design tool because it uses pharmacophores to
guide the placement of fragments. This results in hits that not only complement the protein active site, but
that also complement each other to create realistic new drug leads. This powerful tool can rapidly produce
lists of completely novel compounds that all contain the features thought to be critical for binding to a
specific drug target.
QSAR and ADMET Products
Product
DS ADMET
Description
Get an early assessment of your compounds by calculating the predicted absorption, distribution,
metabolism, excretion and toxicity (ADMET) properties for collections of molecules such as synthesis
candidates, vendor libraries, and screening collections. Use the calculated results to eliminate compounds
with unfavorable ADMET characteristics and evaluate proposed structural refinements, designed to improve
ADMET properties, prior to synthesis. Optimizing these properties during early drug discovery efforts
is critical for reducing problems in later development phase. Included are models for human intestinal
absorption, aqueous solubility, blood brain barrier penetration, plasma protein binding, cytochrome P450
2D6 inhibition, and hepatotoxicity. Filter a set of small molecules and select only those molecules that meet
the rules specified by the set of selected SMARTS® rules.
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DATASHEET: Discovery Studio Science Portfolio
QSAR and ADMET Products (continued)
Product
DS TOPKAT
Description
Evaluate your compounds’ performance in experimental assays and animal models. Compute and validate
assessments of the toxic and environmental effects of chemicals solely from their molecular structure.
TOPKAT (TOxicity Prediction by Komputer Assisted Technology) employs robust and cross-validated
Quantitative Structure Toxicity Relationship (QSTR) models for assessing various measures of toxicity and
utilizing the patented Optimal Predictive Space validation method to assist in interpreting the results.
Examples of Topkat endpoints include:
Ames mutagenicity, Rat Oral LD50, Chronic LOAEL, Skin irritation, Ocular Irritancy, Fathead Minnow LD50,
and a range of NTP and FDA Carcinogenicity test predictions.
DS QSAR BUNDLE
DS QSAR provides easy access to the hundreds of molecular descriptors, proven in biological systems to
correlate with activity. Easily apply modeling techniques such as Bayesian models, multiple linear regression,
Partial Least Squares (PLS), Genetic Functional Analysis (GFA), and more.
DS QSAR PLUS
BUNDLE
DS QSAR Plus is an extension of the DS QSAR product. It includes Genetic Function Approximation (GFA)
regression models, an advanced neural network component and VAMP descriptors, a semi-empirical
quantum mechanical method for rapidly calculating accurate electronic properties for thousands of
candidate compounds.
DS
DMOL3DESCRIPTORS
COMPONENT
The density-functional theory (DFT) program DMol3 can use used for calculating electronic properties of
compounds at a very high level of accuracy.
DS
VAMPDESCRIPTORS
COMPONENT
VAMP descriptors, a semi-empirical quantum mechanical method for rapidly calculating accurate electronic
properties for thousands of candidate compounds.
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DATASHEET: Discovery Studio Science Portfolio
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